In order to accurately control the portable AUV, a dynamic modeling method based on computational fluid dynamics (CFD) and a improved Generalized Predictive Control (GPC) method were presented. First, the whole modeling process was described from two aspects: dynamic model derivation and model parameter identification. Second, the validity of the model and modeling method were tested by comparing the simulation data and experimental data. Finally, based on the mathematical model, the improved GPC method was used to control the portable AUV in the depth plane and heading plane, and the better control performance was obtained.